cannot find libhdf5_hl.so.10

[WeiCSong]

Hi hdf5r developer,when i load an R package(seurat) which depends on hdf5r,i got following error:

Error: package or namespace load failed for ‘Seurat’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/lustre/home/acct-bmelgn/bmelgn-3/spack/opt/linux-centos7-x86_64/gcc-5.4.0/r-3.5.0-tudjrvhf4huss27eyyzgyfx6zwu4nu66/rlib/R/library/hdf5r/libs/hdf5r.so':
libhdf5_hl.so.10: cannot open shared object file: No such file or directory
Execution halted

I can find libhdf5_hl.so.10 under the path of hdf5

"/lustre/home/acct-bmelgn/bmelgn-3/spack/opt/linux-centos7-x86_64/gcc-5.4.0/hdf5-1.8.19-zdptwox2bglutn3rr6ogajzqelodyriz/lib/libhdf5_hl.so.10"

I tried to copy this file to hdf5r library, but didnt help. I wonder why R cant find this file.Wish to learn from you. Thanks!

[chuseq]

See #94

[panxueling]

I had the same problem. It's been solved now.

install.packages("hdf5r")

The following is the output of the software installation:
checking for hdf5_hl.h... yes
checking for H5LTpath_valid in -lhdf5_hl... yes
checking for main in -lhdf5_hl... yes
checking for matching HDF5 Fortran wrapper... /share/software/apps/anaconda2/bin/h5fc
Found hdf5 with version: 1.10.4
checking for ggrep... /usr/bin/grep
checking whether /usr/bin/grep accepts -o... yes
checking for ggrep... (cached) /usr/bin/grep
checking whether /usr/bin/grep accepts -o... yes
Using variables:
HDF5_LIBS= -L/share/software/apps/anaconda2/lib -L/share/software/apps/anaconda2/lib -L/share/software/apps/anaconda2/lib -lrt -lpthread -lz -ldl -lm

find 'HDF5_LIBS= -L/share/software/apps/anaconda2/lib '

linux code: ls /share/software/apps/anaconda2/lib/libhdf5_hl.so.100
vim ~/.bashrc
Added to the end script "export LD_LIBRARY_PATH = $LD_LIBRARY_PATH: / share/software/apps/anaconda2 / lib"
R code: dyn.load("/share/software/apps/anaconda2/lib/libhdf5_hl.so.100")
install.packages("hdf5r")

[mmokrejs]

Thanks to @panxueling , due to

checking for matching HDF5 Fortran wrapper... /share/software/apps/anaconda2/bin/h5fc
...
Using variables:
HDF5_LIBS= -L/share/software/apps/anaconda2/lib -L/share/software/apps/anaconda2/lib -L/share/software/apps/anaconda2/lib -lrt -lpthread -lz -ldl -lm

I realized that in my case wrong (system-wide while outdated) h5cc was being found but the libs were searched elsewhere. After that I could easily reinstall hdf5r and Rhdf5lib.